User contributions
From Phaserwiki
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- 18:40, 5 April 2016 (diff | hist) . . (+267) . . Combined MR-SAD using CCP4i (Suggest using sculptor on the goat model.)
- 16:24, 5 April 2016 (diff | hist) . . (+1,082) . . MR using CCP4i:TOXD (Update to use Sculptor and Ensembler)
- 14:03, 5 April 2016 (diff | hist) . . (+114) . . MR using keyword input (→Searching for more than one molecule: Correct old idea that SEARCH order in script matters.)
- 13:56, 5 April 2016 (diff | hist) . . (-15) . . MR using keyword input (→Adding to the Script: Update script to continue to work, now that multiple PDB files can't be added to ensemble on a single line.)
- 13:43, 5 April 2016 (diff | hist) . . (+272) . . MR using keyword input (→Sample Script: Mention preference for intensities.)
- 15:22, 15 February 2016 (diff | hist) . . (-2) . . Molecular Replacement (→Annotation: Clarify RF++)
- 01:15, 16 January 2016 (diff | hist) . . (+914) . . FAQ (Add warning about the common mistake of using Phaser to "verify" a refined model.) (current)
- 16:19, 27 November 2015 (diff | hist) . . (+1) . . m Keywords (→link=PURGE: Fix spelling)
- 14:56, 25 November 2015 (diff | hist) . . (+97) . . Keywords (→link=MODE: Add mode MR_ELLG)
- 14:51, 25 November 2015 (diff | hist) . . (+44) . . Modes (→Modes: Add sample Python call to mode MR_ELLG)
- 14:48, 25 November 2015 (diff | hist) . . (+240) . . Modes (→Modes: Add mode MR_ELLG)
- 13:05, 25 November 2015 (diff | hist) . . (+424) . . Keywords (→link=TNCS: Update TNCS commands)
- 20:38, 4 November 2015 (diff | hist) . . (+6) . . Python Example Scripts (→Normal Mode Analysis: Fix syntax for NMA, but this still crashes because the modes and the pdb files are not in one-to-one correspondence.)
- 21:33, 3 November 2015 (diff | hist) . . (+4) . . Python Example Scripts (→Anisotropy Correction: Change setREFL_ID to setLABI_F_SIGF)
- 21:09, 3 November 2015 (diff | hist) . . (+7) . . Python Example Scripts (→Translational NCS Analysis: Change setREFL to setREFL_F_SIGF)
- 21:02, 3 November 2015 (diff | hist) . . (+7) . . Python Example Scripts (→Anisotropy Correction: Change setREFL to setREFL_F_SIGF)
- 21:01, 3 November 2015 (diff | hist) . . (+2) . . m Python Example Scripts (→Reading MTZ Files for Experimental Phasing: Comment out name of script in script)
- 20:59, 3 November 2015 (diff | hist) . . (+1) . . Python Example Scripts (→Automated Molecular Replacement: Comment out name of beta_blip_auto.py script in script)
- 20:59, 3 November 2015 (diff | hist) . . (+7) . . Python Example Scripts (→Automated Molecular Replacement: Change setREFL to setREFL_F_SIGF)
- 12:54, 30 October 2015 (diff | hist) . . (0) . . Keywords (→link=HAND: Description of "ON" and "OFF" was reversed)
- 10:33, 8 October 2015 (diff | hist) . . (+11) . . Keywords (→link=TARGET: Minor correction to available rot and tra targets)
- 15:04, 29 June 2015 (diff | hist) . . (+1) . . m Keywords (→link=TNCS: RMS has to be RMSD in TNCS parser)
- 08:57, 10 June 2015 (diff | hist) . . (+38) . . Keywords (→link=OCCUPANCY: Update defaults to agree with current code)
- 08:49, 10 June 2015 (diff | hist) . . (0) . . m Keywords (→link=PACK: typo)
- 08:43, 10 June 2015 (diff | hist) . . (+94) . . Keywords (→link=SEARCH: Clarify pruning algorithm.)
- 07:38, 19 May 2015 (diff | hist) . . (+359) . . Molecular Replacement (→Has Phaser Solved It?: Clarify interpretation of RFZ.)
- 13:58, 14 May 2015 (diff | hist) . . (+174) . . Keywords (→link=PARTIAL: Clarify necessity to carry out MR before MR-SAD.)
- 15:23, 3 February 2015 (diff | hist) . . (+13) . . Keywords (→link=SOLPARAMETERS: Show MINSIGA in equation.)
- 15:18, 3 February 2015 (diff | hist) . . (-47) . . Keywords (→link=SOLPARAMETERS: Replace "s" by "1/d")
- 15:15, 3 February 2015 (diff | hist) . . (+131) . . Keywords (→link=SOLPARAMETERS: Add equation for solvent term for Sigma(A) curve)
- 19:44, 11 November 2014 (diff | hist) . . (+310) . . Molecular Replacement (→Translational Non-crystallographic Symmetry: Some modifications and clarifications)
- 09:48, 11 August 2014 (diff | hist) . . (+321) . . Keywords (→link=PURGE: Clarify interaction with PEAKS command.)
- 09:44, 11 August 2014 (diff | hist) . . (+258) . . Keywords (→link=PEAKS: Clarify that PURGE is usually the command to use.)
- 13:56, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Logfile Handling: Replace setLABI with setLABI_F_SIGF)
- 13:55, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Translational NCS Analysis: Replace setLABI with setLABI_F_SIGF)
- 13:55, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Cell Content Analysis: Replace setLABI with setLABI_F_SIGF)
- 13:54, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Anisotropy Correction: Replace setLABI with setLABI_F_SIGF)
- 13:53, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Automated Molecular Replacement: Replace setLABI with setLABI_F_SIGF)
- 13:53, 3 June 2014 (diff | hist) . . (+7) . . Python Example Scripts (→Reading MTZ Files for Molecular Replacement: Replace setLABI with setLABI_F_SIGF)
- 14:06, 29 May 2014 (diff | hist) . . (+53) . . Keywords (→link=BFACTOR: Correct definition of BFACTOR REFINE SIGMA, update default for SIGMA)
- 09:02, 28 May 2014 (diff | hist) . . (+1) . . Keywords (→link=MACTNCS: Correct syntax, with VRMS instead of VAR)
- 12:25, 23 April 2014 (diff | hist) . . (+158) . . Keywords (→link=ENSEMBLE: Provide guess for RMS for EM maps.)
- 18:14, 10 April 2014 (diff | hist) . . (+772) . . SAD using CCP4i (Add step to carry on building from very incomplete initial model)
- 12:18, 9 December 2013 (diff | hist) . . (-214) . . Molecular Replacement (→"rlist" Files: Remove discussion of degenerate translation search, which is no longer supported.)
- 12:17, 9 December 2013 (diff | hist) . . (-447) . . Molecular Replacement (→"sol" Files: Remove discussion of degenerate 3DIM and 5DIM cases, no longer supported.)
- 12:14, 9 December 2013 (diff | hist) . . (-133) . . Molecular Replacement (→How to Define Solutions: Remove mention of degenerate translation functions, which are no longer supported.)
- 12:12, 9 December 2013 (diff | hist) . . (-542) . . Keyword Example Scripts (→Brute Translation Function: Remove script for degenerate translation function, which is no longer supported.)
- 12:11, 9 December 2013 (diff | hist) . . (-309) . . Keyword Example Scripts (→"rlist" Files: Remove discussion of degenerate translation search, which is no longer supported.)
- 12:09, 9 December 2013 (diff | hist) . . (-365) . . Keyword Example Scripts (→"sol" Files: Remove discussion of degenerate 3DIM and 5DIM cases, no longer supported.)
- 10:54, 4 December 2013 (diff | hist) . . (+26) . . FAQ (Mention st9bad_alloc so that people with out of memory problems will find this web page.)
- 11:26, 2 December 2013 (diff | hist) . . (+194) . . FAQ (Add suggestion to cut final refinement resolution to reduce memory usage if necessary.)
- 15:54, 21 October 2013 (diff | hist) . . (-2) . . m Publications (→Primary Citations: Format LERF citation like the rest (authors after title))
- 15:52, 21 October 2013 (diff | hist) . . (+634) . . Publications (→Primary Citations: Add CCP4 Study Weekend 2013 papers)
- 07:40, 8 October 2013 (diff | hist) . . (+170) . . Molecular Replacement (→What to do in Difficult Cases: Note that brute rotation function can now be used within automated pipeline)
- 07:36, 8 October 2013 (diff | hist) . . (+443) . . FAQ (Update discussion of negative LLG to mention VRMS refinement.)
- 08:11, 22 August 2013 (diff | hist) . . (+4) . . Keywords (→link=SOLPARAMETERS: Add "USE" subkey to default definition for BULK)
- 10:40, 5 August 2013 (diff | hist) . . (+126) . . Keywords (→link=RFACTOR: Note that this test also applies to judging success in MR_ATOM)
- 10:38, 5 August 2013 (diff | hist) . . (+19) . . Keywords (→link=SOLUTION: Mention Euler angle convention here.)
- 10:37, 5 August 2013 (diff | hist) . . (+218) . . Molecular Replacement (→Annotation: Add explanation of Euler angle convention.)
- 09:21, 4 August 2013 (diff | hist) . . (-2) . . Keywords (→link=RFACTOR: Change RESHARP to RFACTOR to RFACTOR description)
- 12:59, 28 June 2013 (diff | hist) . . (0) . . Keywords (→link=TRANSLATE: Footnotes didn't correspond to superscripts)
- 12:55, 28 June 2013 (diff | hist) . . (+2) . . m Keywords (→link=TRANSLATE: add spaces)
- 12:54, 28 June 2013 (diff | hist) . . (+7) . . Keywords (→link=ROTATE: Need VOLUME subkey in ROTATE AROUND option)
- 13:36, 25 June 2013 (diff | hist) . . (-135) . . FAQ (Update advice on memory consumption)
- 21:51, 11 April 2013 (diff | hist) . . (+7) . . m SAD using CCP4i (formatting)
- 21:25, 11 April 2013 (diff | hist) . . (+84) . . SAD using CCP4i (A few more changes to match the current SAD pipeline.)
- 16:03, 10 April 2013 (diff | hist) . . (+726) . . SAD using CCP4i (Update to describe Phaser pipeline instead of old standalone Phaser-EP GUI)
- 16:58, 19 January 2013 (diff | hist) . . (+62) . . Publications (→Primary Citations: Add link to tNCS statistics PDF)
- 16:57, 19 January 2013 (diff | hist) . . (+149) . . Publications (→Primary Citations: Add tNCS statistics paper (add link once file is uploaded))
- 19:15, 23 November 2012 (diff | hist) . . (-2) . . MR using CCP4i:BETA/BLIP (Update for current version of Phaser) (current)
- 19:10, 23 November 2012 (diff | hist) . . (+794) . . Combined MR-SAD using CCP4i (Bring up to date with CCP4 6.3, using Parrot instead of DM and ARP/wARP Classic instead of Expert System)
- 09:48, 8 November 2012 (diff | hist) . . (+399) . . Molecular Replacement (→Has Phaser Solved It?: Add a paragraph about finding a single PDB file.)
- 09:43, 8 November 2012 (diff | hist) . . (+546) . . Molecular Replacement (→Has Phaser Solved It?: Update, clarify.)
- 11:03, 10 October 2012 (diff | hist) . . (-1) . . m Keywords (→link=MACTNCS: Correct subkey "VRMS" to "VAR")
- 10:30, 28 August 2012 (diff | hist) . . (+24) . . m Molecular Replacement (→What Resolution of Data Should be Used?: minor clarification)
- 12:09, 27 August 2012 (diff | hist) . . (0) . . m Keywords (→link=ELLG: Fix typo in link)
- 12:07, 27 August 2012 (diff | hist) . . (+69) . . Keywords (→link=ELLG: Link eLLG to explanation)
- 11:59, 27 August 2012 (diff | hist) . . (+2,402) . . Molecular Replacement (Concept of eLLG and strategies based on it)
- 16:13, 15 August 2012 (diff | hist) . . (+478) . . Bugs (Add description of SGALTERNATIVE LIST bug in CCP4-6.3 version) (current)
- 10:39, 18 May 2012 (diff | hist) . . (+13) . . Keywords (→link=PACK: Clarify description of PACK_CUTOFF)
- 19:21, 17 May 2012 (diff | hist) . . (+9) . . Keywords (→link=PACK: add "PERCENT" to setPACK_SELE choices)
- 10:38, 24 April 2012 (diff | hist) . . (-736) . . Top Ten Tips (Update tips, add some for SAD and both)
- 09:30, 24 April 2012 (diff | hist) . . (+79) . . Publications (→Reviews: add link)
- 09:24, 24 April 2012 (diff | hist) . . (+104) . . Publications (→Reviews: add paper)
- 09:19, 24 April 2012 (diff | hist) . . (+271) . . Events (→2010: add some meetings)
- 09:15, 24 April 2012 (diff | hist) . . (+301) . . Events (→2011: add a few workshops)
- 09:09, 24 April 2012 (diff | hist) . . (-1) . . m Events (→2012)
- 09:07, 24 April 2012 (diff | hist) . . (-11) . . m Events (→2012)
- 09:06, 24 April 2012 (diff | hist) . . (-3) . . m Events (→Upcoming)
- 09:05, 24 April 2012 (diff | hist) . . (+105) . . Events (→2012: add Santa Fe)
- 09:03, 24 April 2012 (diff | hist) . . (+57) . . Events (→Upcoming: add ECM27)
- 11:23, 17 February 2012 (diff | hist) . . (-1) . . Keywords (→link=TNCS: Correct defaults, particularly TNCS USE defaults to ON)
- 10:02, 27 January 2012 (diff | hist) . . (+35) . . Keywords (→link=ENSEMBLE: A bit clearer yet)
- 10:01, 27 January 2012 (diff | hist) . . (+59) . . Keywords (→link=ENSEMBLE: Clarify meaning of "extent")
- 18:21, 18 October 2011 (diff | hist) . . (+1) . . m Keywords (→link=BFACTOR: fix another typo)
- 18:20, 18 October 2011 (diff | hist) . . (-1) . . m Keywords (→link=BFACTOR: fix typo)
- 18:53, 29 September 2011 (diff | hist) . . (+30) . . Keywords (→link=ENSEMBLE: Update information about how CARD option is implemented in non-standard PDB files.)
- 09:47, 28 September 2011 (diff | hist) . . (+461) . . Molecular Replacement (→Has Phaser Solved It?: Update to describe TFZ-equivalent)
- 13:26, 3 August 2011 (diff | hist) . . (+11) . . Downloads (→CCP4i: also Mac)
- 13:25, 3 August 2011 (diff | hist) . . (0) . . Downloads (→Source Code: change 2.1 to 2.3)
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